After coming up empty-handed when they targeted tomatoes, federal health inspectors say that the lone pepper has tested positive for the strain of salmonella that has infected more than 1,250 people since April.

After the contamination was discovered, the Food and Drug Administration on Monday warned consumers against eating any fresh jalapenos while its investigation continues.

The wholesaler that processed the contaminated pepper, Agricola Zaragoza in McAllen, Texas, has recalled all its pepper shipments as a result of the FDA's findings. And restaurants, grocery stores and other food services have been notified of the FDA's stepped-up warning against the fresh peppers as well as fresh salsa or sauces that use jalapenos as ingredients.

Processed, cooked or pickled products are not affected by the warning, so chains like Chipotle Mexican Grill started grilling all their jalapenos last week.

"We're monitoring the ongoing investigation very carefully,'' said Chris Arnold, spokesman for the Denver-based chain. "We'd certainly like to get back to normal."

Dr. David Acheson, the FDA's associate commissioner for foods, said that while finding the genetic match in the jalapeno was a "significant breakthrough," the agency still doesn't know the origin of the salmonella outbreak, which is ongoing.

"Though the pepper was grown on a farm in Mexico, it does not mean the pepper was contaminated in Mexico,'' he said. "We're focusing on the entire chain — the farm, distribution center, packinghouses — and looking at water, soil, work surfaces and packing boxes, to see how it spread to the American consumer."

And while officials lifted the warning against fresh tomatoes last week, they have not ruled out the possibility that tomatoes could have been the initial source of contamination earlier in the outbreak.

"There may be more than one vehicle here,'' said Dr. Robert Tauxe of the Centers for Disease Control and Prevention. "I do not think tomatoes have been exonerated." Tomatoes currently on the market, however, are safe to eat.

Florida growers, who account for nearly half of all fresh tomatoes consumed nationwide, have estimated that the FDA's monthlong warning against their crop cost them millions of dollars in lost sales.

The detective work that led to the Texas border town started with investigators questioning a cluster of people who became ill after eating at the same restaurant, then tracking the produce they had consumed. Agricola Zaragoza, which reportedly had about $600,000 in sales last year, did not return a call for comments.

The FDA said all other samples from the distributor had tested negative for salmonella, but samples are continuing to be analyzed. In addition to jalapenos, the distributor also handles tomatillos.

Though jalapenos are not grown commercially in Florida, there are commercial operations elsewhere on the East Coast. Asked why the FDA would extend its warning to non-Mexican jalapenos, Acheson said peppers contaminated in Texas could easily cross-contaminate peppers further along the distribution chain. "We've got to protect the public health with the science we have today,'' he said. "We're pushing this investigation hard and fast to narrow it as quickly as possible."

Times researcher Caryn Baird contributed to this report. Kris Hundley can be reached at hundley@sptimes.com or (727) 892-2996.